I don't know how others' experiences have stacked up, but it seems top schools show preference to applicants who use their own application -- it seems to show more interest in that particular schools than a mass-mailed common app. Keep this in mind for top-choice schools especially.

But what about schools like Duke and Johns Hopkins, you can use either the common app or their application. In the case of the JHU application, there are two extra long essays that really cannot be used anywhere else. Would it be that important to use their schools application or would the common application work just fine?